A role of the CTCF binding site at enhancer Eα in the dynamic chromatin organization of the Tcra–Tcrd locus

Abstract The regulation of T cell receptor Tcra gene rearrangement has been extensively studied. The enhancer Eα plays an essential role in Tcra rearrangement by establishing a recombination centre in the Jα array and a chromatin hub for interactions between Vα and Jα genes. But the mechanism of the Eα and its downstream CTCF binding site (here named EACBE) in dynamic chromatin regulation is unknown. The Hi-C data showed that the EACBE is located at the sub-TAD boundary which separates the Tcra–Tcrd locus and the downstream region including the Dad1 gene. The EACBE is required for long-distance regulation of the Eα on the proximal Vα genes, and its deletion impaired the Tcra rearrangement. We also noticed that the EACBE and Eα regulate the genes in the downstream sub-TAD via asymmetric chromatin extrusion. This study provides a new insight into the role of CTCF binding sites at TAD boundaries in gene regulation.

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947 Distinct role of the CTCF-binding site in IGF2/H19-ICR and of the differential methylated region in IGF2-promoter 0 in LOI and IGF2-expression in prostate cancer

European Urology Supplements ◽

10.1016/s1569-9056(13)61426-8 ◽

2013 ◽

Vol 12 (1) ◽

pp. e947

Author(s):

T. Dansranjavin ◽

F. Wagenlehner ◽

P. Waliszewski ◽

K. Steger ◽

W. Weidner ◽

...

Keyword(s):

Prostate Cancer ◽

Binding Site ◽

Ctcf Binding ◽

Ctcf Binding Site ◽

Distinct Role ◽

Igf2 Expression

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CTCF function is modulated by neighboring DNA binding factors

Biochemistry and Cell Biology ◽

10.1139/o11-033 ◽

2011 ◽

Vol 89 (5) ◽

pp. 459-468 ◽

Cited By ~ 42

Author(s):

Oliver Weth ◽

Rainer Renkawitz

Keyword(s):

Dna Binding ◽

Binding Site ◽

Zinc Finger ◽

Binding Sites ◽

Zinc Finger Protein ◽

Gene Activation ◽

Ctcf Binding ◽

Paternal Allele ◽

Ctcf Binding Site ◽

Enhancer Blocking

The zinc-finger protein CTCF was originally identified in the context of gene silencing and gene repression (Baniahmad et al. 1990; Lobanenkov et al. 1990). CTCF was later shown to be involved in several transcriptional mechanisms such as gene activation (Vostrov et al. 2002) and enhancer blocking (Filippova et al. 2001; Hark et al. 2000; Kanduri et al. 2000; Lutz et al. 2003; Szabó et al. 2000; Tanimoto et al. 2003; Phillips and Corces 2009; Bell et al. 1999; Zlatanova and Caiafa 2009a, 2009b). Insulators block the action of enhancers when positioned between enhancer and promoter. CTCF was found to be required in almost all cases of enhancer blocking tested in vertebrates. This CTCF-mediated enhancer blocking is in many instances conferred by constitutive CTCF action. For some examples however, a modulation of the enhancer blocking activity was documented (Lutz et al. 2003; Weth et al. 2010). One mechanism is achieved by regulation of binding to DNA. It was shown that CTCF is not able to bind to those binding-sites containing methylated CpG sequences. At the imprinting control region (ICR) of the Igf2/H19 locus the binding-site for CTCF on the paternal allele is methylated. This prevents DNA-binding of CTCF, resulting in the loss of enhancer blocking (Bell and Felsenfeld 2000; Chao et al. 2002; Filippova et al. 2001; Hark et al. 2000; Kanduri et al. 2000, 2002; Szabó et al. 2000; Takai et al. 2001). Not only can DNA methylation interfere with CTCF binding to DNA, it was also shown in one report that RNA transcription through the CTCF binding site results in CTCF eviction (Lefevre et al. 2008). In contrast to these cases most of the DNA sites are not differentially bound by CTCF. Even CTCF interaction with its cofactor cohesin does not seem to differ in different cell types (Schmidt et al. 2010). These results indicate that regulation of CTCF activity might be achieved by neighboring factors bound to DNA. In fact, whole genome analyses of CTCF binding sites identified several classes of neighboring sequences (Dickson et al. 2010; Boyle et al. 2010; Essien et al. 2009). Therefore, in this review we will summarize those results for which a combined action of CTCF with factors bound adjacently was found. These neighboring factors include the RNA polymerases I, II and III, another zinc finger factor VEZF1 and the factors YY1, SMAD, TR and Oct4. Each of these seems to influence, modulate or determine the function of CTCF. Thereby, at least some of the pleiotropic effects of CTCF can be explained.

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Functional signatures of evolutionarily young CTCF binding sites

BMC Biology ◽

10.1186/s12915-020-00863-8 ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Dhoyazan Azazi ◽

Jonathan M. Mudge ◽

Duncan T. Odom ◽

Paul Flicek

Keyword(s):

Binding Site ◽

Mus Musculus ◽

Binding Sites ◽

Ctcf Binding ◽

Ctcf Binding Site ◽

Mus Musculus Domesticus ◽

Transcription Start Sites ◽

Regulatory Architecture ◽

Topologically Associated Domains ◽

The Impact

Abstract Background The introduction of novel CTCF binding sites in gene regulatory regions in the rodent lineage is partly the effect of transposable element expansion, particularly in the murine lineage. The exact mechanism and functional impact of evolutionarily novel CTCF binding sites are not yet fully understood. We investigated the impact of novel subspecies-specific CTCF binding sites in two Mus genus subspecies, Mus musculus domesticus and Mus musculus castaneus, that diverged 0.5 million years ago. Results CTCF binding site evolution is influenced by the action of the B2-B4 family of transposable elements independently in both lineages, leading to the proliferation of novel CTCF binding sites. A subset of evolutionarily young sites may harbour transcriptional functionality as evidenced by the stability of their binding across multiple tissues in M. musculus domesticus (BL6), while overall the distance of subspecies-specific CTCF binding to the nearest transcription start sites and/or topologically associated domains (TADs) is largely similar to musculus-common CTCF sites. Remarkably, we discovered a recurrent regulatory architecture consisting of a CTCF binding site and an interferon gene that appears to have been tandemly duplicated to create a 15-gene cluster on chromosome 4, thus forming a novel BL6 specific immune locus in which CTCF may play a regulatory role. Conclusions Our results demonstrate that thousands of CTCF binding sites show multiple functional signatures rapidly after incorporation into the genome.

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222 METHYLATION OF THE 52-UPSTREAM REGION OF THE H19 GENE IN MOUSE SOMATIC CELL, GAMETES, WILD TYPE AND ANDROGENETIC ES CELLS

Reproduction Fertility and Development ◽

10.1071/rdv17n2ab222 ◽

2005 ◽

Vol 17 (2) ◽

pp. 261

Author(s):

H. Kato ◽

H. Murakami ◽

M. Kawasumi ◽

T. Kunieda ◽

M. Okuno ◽

...

Keyword(s):

Genomic Imprinting ◽

Binding Sites ◽

Es Cells ◽

Ctcf Binding ◽

Upstream Region ◽

Ctcf Binding Site ◽

Cpg Sites ◽

Maternal Genome ◽

H19 Gene

In mammals, several genes influenced by the phenomenon of genomic imprinting are critical during development. Recently, Kono et al. (2004 Nature 428, 860–864) reported the production of intact female mouse individuals that had only two haploid sets of maternal genome. They obtained these mice by combining a normal haploid maternal genome and a mutant haploid maternal genome with a 13 k base deletion in the H19 gene and its 5′-upstream region. This genomic combination resulted in the appropriate expression of the Igf2, H19, and other imprinted genes. In the mouse genome, there are four CTCF-binding sites in the 5′-upstream region of the H19 gene. The binding of CTCF to these binding sites regulates the expression of the Igf2 and H19 genes. The binding of CTCF to its binding sites is regulated by methylation of CpG sites in binding sites. In this study, as the first step to elucidate the role of the paternal genomic imprinting during development, we investigated the methylation of CpG sites in the 5′-upstream region of the H19 gene in mouse somatic cells, gametes, and two types of ES cells. Genomic DNA was isolated from BDF1 (C57BL/6N × DBA/2N) mouse's tail (male and female somatic tissue, mST and fST, respectively), spermatozoa (S), oocytes (O), and wild type and androgenetic embryonic stem cells (wtES and agES, respectively). The methylation of CpG sites was evaluated by using the bisulfite sequencing assay. There were 13 CpG sites and a CTCF-binding site in the region from −4413 to −3976 in the H19 gene relative to the transcription start site. The percentages of CpG sites in this region that were methylated were 88% (160/182), 79% (27/130), 93% (230/247), 8% (10/130), 77% (10/13) and 89% (314/351) for mST, fST, S, O, wtES, and agES, respectively. In the CTCF-binding site core motif (CCGCGTGGTGGCAG), the percentages of methylated CpG sites were 93% (26/28), 80% (16/20), 95% (36/38), 0% (0/20), 50% (1/2) and 96% (52/54) for mST, fST, S, O, wtES, and agES, respectively. The CpG sites in the sequence of agES were highly methylated similar to the finding in spermatozoa. However, an aberrant methylation pattern was observed in some clones of agES. From these results, it was concluded that the methylation of CpG sites in the genomic sequence of agES was well conserved and, therefore, agES is useful to elucidate the role of the paternal genomic imprinting during development. This work was supported by Wakayama Prefecture Collaboration of Regional Entities for the Advanced of Technological Excellence, Japan, and by a Grant-in-Aid for the 21st Century COE Program of the Japan MEXT.

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3'HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression

10.1101/2021.05.18.444713 ◽

2021 ◽

Author(s):

Pamela Himadewi ◽

Xue Qing David Wang ◽

Fan Feng ◽

Haley Gore ◽

Yushuai Liu ◽

...

Keyword(s):

Binding Site ◽

Progenitor Cells ◽

Globin Gene ◽

Fetal Hemoglobin ◽

Ctcf Binding ◽

Ctcf Binding Site ◽

Distal Enhancer ◽

Erythroid Progenitor ◽

Hematopoietic Stem ◽

Ctcf Site

Mutations in the adult β-globin gene can lead to a variety of hemoglobinopathies, including sickle cell disease and β-thalassemia. An increase in fetal hemoglobin expression throughout adulthood, a condition named Hereditary Persistence of Fetal Hemoglobin (HPFH), has been found to ameliorate hemoglobinopathies. Deletional HPFH occurs through the excision of a significant portion of the 3 prime end of the β-globin locus, including a CTCF binding site termed 3'HS1. Here, we show that the deletion of this CTCF site alone induces fetal hemoglobin expression in both adult CD34+ hematopoietic stem and progenitor cells and HUDEP-2 erythroid progenitor cells. This induction is driven by the ectopic access of a previously postulated distal enhancer located in the OR52A1 gene downstream of the locus, which can also be insulated by the inversion of the 3'HS1 CTCF site. This suggests that genetic editing of this binding site can have therapeutic implications to treat hemoglobinopathies.

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Indomethacin Increases Quercetin Affinity for Human Serum Albumin: A Combined Experimental and Computational Study and Its Broader Implications

International Journal of Molecular Sciences ◽

10.3390/ijms21165740 ◽

2020 ◽

Vol 21 (16) ◽

pp. 5740

Author(s):

Hrvoje Rimac ◽

Tana Tandarić ◽

Robert Vianello ◽

Mirza Bojić

Keyword(s):

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Binding Site ◽

Binding Sites ◽

Quantum Chemical ◽

Computational Study ◽

The Body ◽

Active Concentration ◽

Insight Into

Human serum albumin (HSA) is the most abundant carrier protein in the human body. Competition for the same binding site between different ligands can lead to an increased active concentration or a faster elimination of one or both ligands. Indomethacin and quercetin both bind to the binding site located in the IIA subdomain. To determine the nature of the HSA-indomethacin-quercetin interactions, spectrofluorometric, docking, molecular dynamics studies, and quantum chemical calculations were performed. The results show that the indomethacin and quercetin binding sites do not overlap. Moreover, the presence of quercetin does not influence the binding constant and position of indomethacin in the pocket. However, binding of quercetin is much more favorable in the presence of indomethacin, with its position and interactions with HSA significantly changed. These results provide a new insight into drug-drug interactions, which can be important in situations when displacement from HSA or other proteins is undesirable or even desirable. This principle could also be used to deliberately prolong or shorten the xenobiotics’ half-life in the body, depending on the desired outcomes.

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